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The Time to Get Started is Now More to see More to understand Here’s why you should partner with Illumina. More with multiomics Our multiomics reagents, equipment and protocols have been validated with hundreds of publications in high-impact, peer-reviewed journals. Integrating multiomics into biological research (https://pubmed.ncbi.nlm.nih.gov/?term=illumina+sequencing) provides scientists with novel scientific insights that make groundbreaking new Illumina’s technology has the broadest range of applications to enable multiomic analyses discoveries possible. on one device and are built to support emerging changes in the multiomics landscape. Illumina supports over 10,000 labs across 115 countries. 24/7 technical support professionals are ready to help you with any project. Need a crash-course on a topic? We have an extensive library of free online training resources to support your research. (https://support.illumina.com/training.html) Learn more about the power of multiomics. Download our free ebook: https://www.illumina.com/more-with-multiomics5

What is Multiomics? Why Multiomics? Multiomics explores multiple “omes” — combinations of the genome, proteome, Biological regulation is complex, and phenotypes are influenced by a myriad of factors that extend transcriptome, and epigenome — in one experiment. beyond DNA. An unbiased characterization of the cellular and environmental factors that influence genotypes and phenotypes is necessary to comprehensively understand novel systems. Proteomics explores protein expression to understand cellular phenotypes and function. Integration of multiomics accelerates: • Discovery of novel associations between biological entities Transcriptomics studies the complete set of RNA transcripts • Identification of relevant biomarkers produced by a genome. • The development of effective therapies Epigenetics looks at how cells control gene activity Multi-Modal Approaches in Multiomics through processes like DNA methylation. Multiomics allows you to explore different modalities (data types such as DNA, Genomics focuses on the structure, function, evolution, RNA and protein) simultaneously by leveraging three main experimental approaches: mapping and editing of information in an organism’s DNA. bulk analysis, single-cell analysis, and spatial analysis (see Figure 2 below). Figure 1: Individual “omes” can be studied in combination. Popular Multiomics Combinations • Bulk analysis: Analyzes pooled cell populations, tissue sections, Multiomics Implications or biopsies in bulk for greater Starting Material Combination efficiency. Genotypes can offer information on susceptibility to diseases. Incorporating RNA sequencing Method Bulk analysis Spatial Single-cell Genomics + helps researchers measure the functional consequences of genetic variation and may reveal • Single-cell analysis: Generates sequencing analysis Transcriptomics therapeutically-exploitable expression patterns. a high-resolution, multiomic understanding of individual cells Genomics + This multiomic approach connects a genotype to the phenotype for more informed research and their functions, interactions, Proteomics into a disease state. and dynamic behavioral events. Transcriptomics + RNA sequencing interrogates gene expression patterns that differentiate cells or distinct • Spatial analysis (aka spatial Expected Data Proteomics cell populations. Incorporating protein detection can link cell-specific expression with genomics): A new frontier in protein biomarkers. molecular biology that captures Average of Average of all Different cell types Genomics + the genomic information of all Cells cells in an area and characteristics Epigenomics Combining epigenomic findings with genetic information allows researchers to understand single cells within their native patterns of gene regulation and how they connect with the genotypes underlying diseases. tissue environment. Transcriptomics + Combining epigenomics and transcriptomics allows researchers to directly measure the ties Figure 2: Multi-modal approaches in multiomics Epigenomics between gene regulation and gene expression. Danny Wells, PhD Single “omic”s can be useful for straightforward There are a variety of insights we’ve gained using Ben Humphreys, MD, PhD questions, but in topics like immunotherapy resistant a multiomics approach that we wouldn’t have if we Scientific Co-Founder and cancer, you want to have as much information as had just used a single modality. Chief of the Division of Nephrology Senior Vice President of possible. That’s where multiomics really shines. Strategic Research, Immunai at Washington University, St. Louis

What Does A Multiomics Workflow Look Like? Genomics and transcriptomics workflows for bulk analysis. Although the details differ depending on A library is a collection of similarly sized nucleic Sample prep Sequencing Secondary analysis Tertiary analysis the “omes” you want to explore, multiomics acid fragments with known adapter DNA workflows generally start with nucleic acid sequences added to the 5’ and 3’ ends. Sample Whole ILMN DNA DRAGEN Germline isolation from which nucleic acid libraries or preparation enables sample compatibility with Genome PCR-Free Prep samples are then prepared. Illumina sequencers and arrays. Following this, data Sequencing DRAGEN Somatic readouts are collected and then analyzed. ILMN DNA Prep (Cancer Research) Genomics (For FFPE Samples) NovaSeq™ 6000 Bulk-Cell Whole ILMN DNA Prep DRAGEN Exome with Enrichment Enrichment Sequencing DRAGEN RNA Nucleic acid Sample Prep Sequencing Analysis isolation or arrays DRAGEN Differential BaseSpace™ Expression Correlation Engine Trancriptomics Whole ILMN Stranded NovaSeq™ 6000 + Transcriptome Total RNA Prep NextSeq™ 2000 with Ribo-Zero Plus + Reagents Sequencing Minoli Perera, PharmD, PhD Multiomics increases our understanding of ILMN Stranded DRAGEN RNA biological mechanisms…which may lead to the mRNA Prep Associate Professor discovery of new drug targets that may prevent DRAGEN Differential Northwestern University adverse events in specific populations. ILMN RNA Prep Expression Feinberg School of Medicine with Enrichment (For FFPE samples) mRNA Sequencing Most popular multiomic Epigenetics/trascriptomics/proteomics workflow for bulk analysis. combinations/workflows Assay for transponsable-accessible chromatin sequencing (ATAC-Seq) and bulk epitope and Workflow key nucleic acid seqeuncing (BEN-Seq) workflows. DNA library prep (Illumina®) Sample prep Sequencing Secondary analysis Tertiary analysis RNA library prep (Illumina®) Proteomics Epigenomics ATAC ILMN Tagment DNA Open Source BaseSpace™ Sequencing instrument/reagents (Illumina®) Non-Illumina products Sequencing TDE1 Enzyme and Tools Correlation Engine Non-Illumina secondary analysis software Secondary analysis software (Illumina®) Non-Illumina tertiary analysis software Buffer Kits Bowtie 2 Burrows-Wheeler Tertiary analysis software (Illumina®) Bulk-Cell Alignment Tool Transcriptomics TotalSeq -A Reagents NovaSeq™ 6000 + + Proteomics NextSeq™ 2000 ILMN Stranded + Reagents mRNA Prep BEN Open Source Tools Sequencing ILMN RNA Prepwith DESeq2 Enrichment (For FFPE samples)

Workflows for methylation arrays Single cell analysis workflows Methylation arrays enable quantitative interrogation of selected methylation sites across the genome and epigenome. Cellular Indexing of Transcriptomes and Epitopes (CITE-Seq) and proteo-genomics. Sample prep Microarrays Secondary analysis Tertiary analysis Sample prep Sequencing Secondary analysis Tertiary analysis InfiniumTM TotalSeq –A, B or C Multiomics Analysis Software (MAS) MethylationEPIC Kit Reagents (human samples) Single-Cell BD AbSeq Assay Transcriptomics Epigenomics + Proteomics CITE-Seq NovaSeq™ 6000 + Array NovaSeq v1.5 Reagents SeqGeq Software InfiniumTM Mouse NextSeq™ 2000 Bulk-Cell Methylation Array Single-Cell + Reagents (murine samples) Immune Profiling GenomeStudio BaseSpace™ Software Correlation Engine iScan Single-CellGene CellRanger Software Expression InfiniumTM Global Diversity Array-8 Kit Genomics Proteo- TotalSeq - + Proteomics genomics D Reagents (high throughput for human samples) Tapestri Platform NextSeq™ 2000 + Tapestri Pipeline Tapestri Single- Reagents Tapestri Insights Genotyping Array Cell Panels InfiniumTM Global Screening Array-24 Kit (high throughput for human samples) Spatial analysis workflow Single cell analysis workflow combining ATAC sequencing with mRNA sequencing Cellular Indexing of Transcriptomes and Epitopes (CITE-Seq) Sample prep Sequencing Secondary analysis Tertiary analysis Sample prep Sequencing Secondary analysis Tertiary analysis Spatial Visium Spatial Gene Visium Spatial Single-Cell Open Source Tools Open Source Tool Expression. Gene Expression Epigenomics Bowtie 2 Seurat by the Satija Transcriptomics + Transcriptomics + Proteomics GeoMx® –Spatial Biology ATAC-Seq + Burrows-Wheeler Lab at New York Data Analysis mRNA-Seq Alignment Tool Genome Center CITE-Seq NovaSeq™ 6000 + Chromium Single DRAGEN NovaSeq v1.5 Reagents Cell Multiome ATAC Single-Cell RNA + Gene Expression NovaSeq™ 6000 + GeoMx® Digital NextSeq™ 2000 NextSeq™ 2000 Spatial Profiler + Reagents + Reagents 10X Genomics GeoMx RNA Assays Cell Ranger/Loupe Browser GeoMx Protein Assays